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- PDB-7dtr: Structure of an AcrIF protein -

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Basic information

Entry
Database: PDB / ID: 7dtr
TitleStructure of an AcrIF protein
ComponentsAcrIF24
KeywordsVIRAL PROTEIN / HTH motif / protein interaction
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsYue, F. / Peipei, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31822012 China
CitationJournal: Nat Commun / Year: 2022
Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24.
Authors: Lingguang Yang / Laixing Zhang / Peipei Yin / Hao Ding / Yu Xiao / Jianwei Zeng / Wenhe Wang / Huan Zhou / Qisheng Wang / Yi Zhang / Zeliang Chen / Maojun Yang / Yue Feng /
Abstract: CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the ...CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the crRNA-guided surveillance (Csy) complex. The HTH motif of AcrIF24 can bind the Acr promoter region and repress its transcription, suggesting its role as an Aca gene in self-regulation. AcrIF24 forms a homodimer and further induces dimerization of the Csy complex. Apart from blocking the hybridization of target DNA to the crRNA, AcrIF24 also induces the binding of non-sequence-specific dsDNA to the Csy complex, similar to AcrIF9, although this binding seems to play a minor role in AcrIF24 inhibitory capacity. Further structural and biochemical studies of the Csy-AcrIF24-dsDNA complexes and of AcrIF24 mutants reveal that the HTH motif of AcrIF24 and the PAM recognition loop of the Csy complex are structural elements essential for this non-specific dsDNA binding. Moreover, AcrIF24 and AcrIF9 display distinct characteristics in inducing non-specific DNA binding. Together, our findings highlight a multifunctional Acr and suggest potential wide distribution of Acr-induced non-specific DNA binding.
History
DepositionJan 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AcrIF24


Theoretical massNumber of molelcules
Total (without water)18,5881
Polymers18,5881
Non-polymers00
Water2,684149
1
A: AcrIF24

A: AcrIF24


Theoretical massNumber of molelcules
Total (without water)37,1762
Polymers37,1762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)77.689, 77.689, 145.121
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein AcrIF24


Mass: 18587.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 2-propanol, imidazole pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15917 / % possible obs: 99.35 % / Redundancy: 29.2 % / CC1/2: 0.998 / Net I/σ(I): 16.8
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 1545 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.84 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 800 5.08 %
Rwork0.2149 14960 -
obs0.2158 15760 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.72 Å2 / Biso mean: 33.3362 Å2 / Biso min: 11.27 Å2
Refinement stepCycle: final / Resolution: 2.1→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 0 150 1421
Biso mean---34.54 -
Num. residues----163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.230.23871220.23082382250498
2.23-2.40.23751290.230324402569100
2.4-2.640.22751270.222724712598100
2.64-3.020.27111270.220724852612100
3.02-3.810.26541290.214725292658100
3.81-38.840.20021660.2012653281999

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